Hi, just to clarify one point on the GUI. You can click or unclick the option "use hydrogens during refinement" on the first tab in i2 GUI in the options field. As indicated it used it only during refinement and does not put it into the output pdb. In the output tab you can choose what should happen with the output of hydrogens, e.g. in file, not in file or default. The default should be actually no, but changing it explicitly to no should do the trick, otherwise there is a bug.
Best Christian On Tue, May 17, 2022 at 9:59 AM Luca Mazzei <luca.mazz...@unibo.it> wrote: > Hello, > > just to clarify, I do not use H atoms for refinement, but as idealised > riding H atoms. In the old-style GI of Refmac one could use riding > hydrogens during refinement without adding them in the output coordinate > file. I do not find this option in the new GI of the CCP4i2 window. As a > result from a a REFMAC job, the ouput PDB file does not contain H atoms, > while the mmcif output file does. At the end of the story, I ran pdbx/mmcif > to convert the PDB in a mmcif file that does not contain H atoms anymore. > It seems to work. > > Best regards > > Luca Mazzei > > > Luca Mazzei - PhD > Laboratory of Bioinorganic Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > Tel: +39 0512096235 > > > > > Il giorno 16 mag 2022, alle ore 15:43, Luca Mazzei <luca.mazz...@unibo.it> > ha scritto: > > Dear CCP4 people, > > Refining a 1.7 Angstroem structure with REFMAC (CCP4i2) using hydrogens > during refinements by generating riding hydrogens I obtain a PDB file that > does not contain H atoms. However, the corresponding mmcif file that I > should use for deposition contains their coordinates and give them either > full or zero occupancy. Do you know how I can safely delete H atoms from > the mmcif file prior deposition? Would this affect Rwork and Rfree > calculated upon validation on the wwPDB? > > Thanks in advance, > > Luca Mazzei > > > Luca Mazzei - PhD > Laboratory of Bioinorganic Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > Tel: +39 0512096235 > > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
